PROJECT SUMMARY/ABSTRACT Genome-wide association studies (GWAS) of complex, multifactorial traits have identified many autosomal susceptibility loci, but the associated variants do not account for a significant proportion of the risk for complex diseases. This may be due in part to additional genetic risk factors that reside in other compartments of the genome, particularly the mitochondrial and X chromosomes. Currently, the role of mitochondrial DNA (mtDNA) and X chromosome variation in complex traits remains largely unknown because the vast majority of GWAS have omitted both or incorrectly analyzed X-linked data. Understanding the role of mtDNA and X chromosome variation in complex phenotypes can provide insight into parent-of-origin, as well as ethnic- and sex-specific, mechanisms of disease. To investigate these phenomena, immune-mediated diseases serve as the perfect paradigm. The prevalence of these highly heritable complex, multifactorial disorders, such as asthma and autoimmune diseases, can depend on parental disease risk status, ethnic background, and/or sex. The maternally-inherited and ethnic and geographically-restricted nature of mitochondrial haplotypes and the sex-specific regulatory mechanisms of X chromosome genes may contribute to such biases in immune- mediated disease risk. Therefore, this study aims to understand the role of mitochondrial and X chromosomal variation on the genetic architecture of complex traits by determining the impact of mitochondrial variation and mitochondrial-nuclear epistasis on asthma risk in a multi-ethnic cohort, and by evaluating the maintenance of X chromosome inactivation of immune-related genes in response to innate and adaptive immune stimulation in peripheral blood leukocytes from members of the Hutterite community of South Dakota. First, to understand the strong maternal risk for childhood onset asthma, in Aim 1, I will test if variation in the mitochondrial genome is associated with asthma in ~6000 children of European, African, Mexican, Puerto Rican, and African Caribbean descent from North America and whether these associations are more pronounced in asthmatic children with asthmatic mothers. In Aim 2, I will test the hypothesis that interactions between mitochondrial and nuclear loci contribute to asthma risk at global and local levels in the genomes of admixed human populations of African ancestry. Finally, to explore sex differences in immune responses, in Aim 3, I will examine X chromosome inactivation by changes in DNA methylation at promoters of X-linked genes in females, and by sex-biased gene expression in immune-stimulated peripheral blood leukocytes in 62 male and 82 female South Dakota Hutterites. Elucidating the role of mtDNA and X chromosomal variation in complex phenotypes will provide insight into the biases in risk of immune-mediated diseases, and ultimately on the genetic architecture of complex phenotypes.